Example of the .ndb file format is presented below. There is a binary format called .cndb.
Scripts to convert from .cndb and .ndb to .pdb, .gro and . spw can be found here.
Details of each NDB file format entry are described here.

HEADER            NDB File Format Example                      Dec-19
TITLE             The Nucleome Data Bank: Web-based Resources
TITLE             2 Simulate and Analyze the Three-Dimensional Genome
EXPDTA            Simulation - MEGABASE - MiChroM
AUTHOR            Contessoto et. al. - 2019
CYCLE             INTERPHASE     G2
SEQCHR    1  1P     5  A2 B1 B3 A1 B4
SEQCHR    1  1M     5  B2 B3 A1 B3 B1
MODEL     0
CHROM           1 A2  ctcf+   1P          1    0.372   -0.929    0.394            1       50000    1.000
CHROM           2 B1          1P          2    0.410   -0.117    0.953        50001      100000    1.000
CHROM           3 B3          1P          3    0.318    0.857    0.866       100001      150000    1.000
CHROM           4 A1  ctcf-   1P          4    0.321   -0.939    0.272       150001      200000    1.000
CHROM           5 B4          1P          5    1.193    0.923   -0.776       200001      250000    1.000
CHROM           6 B2          1M          1    1.124    0.908   -0.659            1       50000    1.000
CHROM           7 B3  ctcf-   1M          2    0.324    0.068   -0.386        50001      100000    1.000
CHROM           8 A1          1M          3   -0.327    0.701   -0.096       100001      150000    1.000
CHROM           9 B3          1M          4   -0.581   -0.013    0.432       150001      200000    1.000
CHROM          10 B1          1M          5   -0.936   -0.850    0.239       200001      250000    1.000
DNAELE         11 TF           2          1   -1.409   -0.888   -0.631       150001      150500    0.100
DNAELE         12 CH           3          1    0.352   -0.935    0.354            1      200000    0.100
...
LOOPS  1     4     COHESIN
LOOPS  5     6     POLYCOMB
END